[Pilotdave]

Theo, if your wiring at the cutout is as you describe in #11, you don't need to polarize the generator. You do need to fix that wiring by connecting the wire from the generator to the other terminal on the cutout. You also need to reverse the wires attached to your ammeter posts as they are likely reversed. You can run the car this way but would want to fix this so the ammeter reads properly.

Here's what it sounds like could have been happening:

Your generator is essentially an electric motor. If you were to connect a generator directly to a battery on your workbench, the generator would spin just as a motor does. With your cutout wired incorrectly as you describe in #11, you have no switch to disconnect your battery from the generator when the engine is not running. Your battery would be trying to spin the generator whenever the engine is not running. This runs down your battery. With the engine running, you would be charging the battery though the incorrectly wired ammeter is telling you otherwise. However, your battery likely would be losing charge faster while the engine is off than you can recharge it while driving. So over time - and not too much at that - your battery will lose enough charge to no longer start your car. You could then recharge your battery and repeat the cycle.